Publications

Under peer review:

• Joint distribution of nuclear and cytoplasmic mRNA levels in stochastic models of gene expression: analytical results and parameter inference
  Y. Wang, J. Szavits-Nossan, Z. Cao and R. Grima
  bioRxiv 2024.04.29.591679 (2024), 17pp

• Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression
  A. G. Nicoll, J. Szavits-Nossan, M. R. Evans, R. Grima
  biorxiv:2023.12.30.573521 (2023), 33pp

Peer-reviewed:

1. Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction
   M. Ma, J. Szavits-Nossan, A. Singh, R. Grima
   Accepted for publication in Mathematical Biosciences (2024), 49pp

2. Solving stochastic gene expression models using queueing theory: a tutorial review
   J. Szavits-Nossan and R. Grima
   Biophysical Journal 123(9), 1034-1057 (2024), 32pp
   Literature Review

3. TASEPy: a Python-based package to iteratively solve the inhomogeneous exclusion process
   L. Ciandrini, R. L. Crisostomo and J. Szavits-Nossan
   SciPost Phys. Codebases 22 (2023), 23pp

4. Uncovering the effect of RNA polymerase steric interactions on gene expression noise: analytical distributions of nascent and mature RNA numbers
   J. Szavits-Nossan and R. Grima
   Phys. Rev. E 108, 034405 (2023), 22pp

5. Stochastic scanning events on the GCN4 mRNA 5’ untranslated region generate cell-to-cell heterogeneity in the yeast nutritional stress response
   X. Meng, A. Reed, J. Szavits-Nossan and J. McCarthy
   Nucleic Acids Research gkad433 (2023), 12pp

6. Steady-state distributions of nascent RNA for general initiation mechanisms
   J. Szavits-Nossan and R. Grima
   Phys. Rev. Research 5, 013064 (2023), 13pp

7. Mean-field theory accurately captures the variation of copy number distributions across the mRNA’s life cycle
   J. Szavits-Nossan and R. Grima
   Phys. Rev. E 105, 014410 (2022), 15pp
   Editors’ Suggestion

8. Current-density relation in the exclusion process with dynamic obstacles
   J. Szavits-Nossan and B. Waclaw
   Phys. Rev. E 102, 042117 (2020), 11pp

9. Inferring efficiency of translation initiation and elongation from ribosome profiling
   J. Szavits-Nossan and L. Ciandrini
   Nucleic Acids Research 48(17), 9478–9490 (2020), 13pp

10. Dynamics of ribosomes in mRNA translation under steady and non-steady state conditions
    J. Szavits-Nossan and M. R. Evans
    Phys. Rev. E 101, 062404 (2020), 12pp

11. Power series method for solving TASEP-based models of mRNA translation
    S. Scott and J. Szavits-Nossan
    Phys. Biol. 17, 015004 (2020), 16pp

12. Power series solution of the inhomogeneous exclusion process
    J. Szavits-Nossan, M. Carmen Romano and L. Ciandrini
    Phys. Rev. E 97, 052139 (2018), 13pp

13. Deciphering mRNA sequence determinants of protein production rate
    J. Szavits-Nossan, L. Ciandrini and M. Carmen Romano
    Phys. Rev. Lett. 120, 128101 (2018), 6pp

14. Conditioned random walks and interaction-driven condensation
    J. Szavits-Nossan, M. R. Evans and S. N. Majumdar
    J. Phys. A: Math. Theor. 50 024005 (2017), 28 pp
    Selected for the “Emerging Talents” collection

15. Inequivalence of nonequilibrium path-ensembles: the example of stochastic bridges
    J. Szavits-Nossan and M. R. Evans
    J. Stat. Mech. P12008 (2015), 22 pp

16. A kinetic study of ovalbumin fibril formation: the importance of fragmentation and end-joining
    J. M. D. Kalapothakis, R. J. Morris, J. Szavits-Nossan, K. Eden, S. Covill, S. Tabor, J. Gillam, P. E. Barran, R. J. Allen and C. E. MacPhee
    Biophys. J. 108(9), 2300–2311 (2015), 12pp

17. Condensation transition in joint large deviations of linear statistics
    J. Szavits-Nossan, M. R. Evans and S. N. Majumdar
    J. Phys. A: Math. Theor. 47, 455004 (2014), 31pp
    Selected for the “Highlights of 2014” collection

18. Inherent variability in the kinetics of autocatalytic protein self-assembly
    J. Szavits-Nossan, K. Eden, R. J. Morris, C. E. MacPhee, M. R. Evans and R. J. Allen
    Phys. Rev. Lett. 113, 098101 (2014), 5pp

19. Constraint-driven condensation in large fluctuations of linear statistics
    J. Szavits-Nossan, M. R. Evans and S. N. Majumdar
    Phys. Rev. Lett. 112, 020602 (2014), 5pp

20. Disordered exclusion process revisited: some exact results in the low-current regime
    J. Szavits-Nossan
    J. Phys. A: Math. Theor. 46, 315001 (2013), 24pp

21. Absence of phase coexistence in disordered exclusion processes with bypassing
    J. Szavits-Nossan and K. Uzelac
    J. Stat. Mech. P05030 (2011), 18pp

22. Impurity-induced shocks in the asymmetric exclusion process with long-range hopping
    J. Szavits-Nossan and K. Uzelac
    J. Stat. Mech. P12019 (2009), 13pp

23. Scaling properties of the asymmetric exclusion process with long-range hopping
    J. Szavits-Nossan and K. Uzelac
    Phys. Rev. E 77, 051116 (2008), 8pp

24. Totally asymmetric exclusion process with long-range hopping
    J. Szavits-Nossan and K. Uzelac
    Phys. Rev. E 74, 051104 (2006), 8pp

Doctoral thesis:

Phase transitions in driven diffusive systems far from equilibrium
University of Zagreb (2011), 118pp